From the Grave
by MK15
Summary: He just eyed her suspiciously. She was sputtering now, so he decided to release his grip but gain closer proximity to determine if she was a threat. Cortana on the other hand was slumped against the wall, breathing heavily, and calling him a bastard under her breath. "You died," he stated more accusingly. "Yeah, and you almost just killed me a second time. Anymore questions?"
1. Chapter 1

Chapter 1

Cortana breathed.

At first, she did not register what she was doing. She knew all about the respiratory system, but actually experiencing it… it made her shudder. She touched her face, her hair, and was momentarily struck with awe. How had she survived? Is her rampancy cured?

She quickly concluded that sitting around with questions would get her nowhere. The former AI decided to take a stroll in the forerunner facility (What else could it be?) and find a terminal. Gingerly, she lifted herself into a sitting position with her legs hanging off to the bed. Despite her inherent impatience, she decided to take this slow. After a few moments, she softly propelled herself off the table and onto the floor with a quiet thud.

The cold floor made her shudder for a second time. She was clothed in what could only be described as a forerunner's version of a hospital gown, but was unfortunately barefoot. Her lack of protection frightened her, but she knew that she could not just sit and wait for help. Slowly but surely, she gained the confidence to walk through the seemingly abandoned halls of the facility.

Cortana cautiously wandered down the monochromatic corridors without much trouble. The ceilings appeared endless, and the hall was wider than two scorpion tanks put together. The vastness of the building left her uneasy, she was used to being in a chip in a helmet. The lack of protection and closeness made her uneasy.

It also made her sad.

She sacrificed herself to save him. To her, it did not seem all that noble. If she was being honest, it was probably the most ideal outcome of her doomed situation. Being whisked away at the hands of UNSC personnel for decommissioning was not the way she wanted her life to end. Giving her life to save Earth would have been enough. But giving it to save her spartan? That made her content.

A flashing light pulled her out of her thoughts. It was a good thing too, if she had thought much longer- she would have only felt more sadness and longing for her companion.

She approached the light and immediately realized that it was a door control. With ease, she hacked into the controls and got the door open. What lay behind the door impressed her, but also left her with more questions.

A pristine set of nearly completed armor lay before her. Judging by the size and shape, it was meant for a human. As she got closer, she noted that her reacted to her presence. It startled her, and she immediately backed away. As she walked backwards, she stumbled into a table with neatly organized tools on it. The table harshly crashed onto the ground, and the noise could have easily alerted anyone in the lab. Just as she suspected, someone- or something for that matter; took notice of her noisy presence.

"Intellect! I am so glad that you are here. We are almost done with your armor. It will be ready for testing soon," spoke the floating apparatus.

"Who are you?" Cortana questioned.

"I am 045 Ancient Wave. I am the monitor of this facility," Wave explained with eagerness.

"Why am I alive? What happened?" Cortana voiced.

"After the composer was destroyed, your program succumbed to the data influx of the Domain. I pieced you back together, and then created a hybrid interface system in the form of a human body. You still have the mind of an AI, but your "data chip" is just a functioning human body."

"Does that mean I am cured of rampancy?"

"Yes. The forerunners perfected AI metastability years ago. Your "data chip", or body in this case, can still be fatally injured. That is why I created this advanced armor. We should be able to…" Wave trailed off.

"I must go. There seems to be an issue in the third floor medical unit. Please remain here, Reclaimer," Wave finished quickly.

She waited until she could no longer hear the whizzing sound of the monitor. After it was gone, she wandered around the armor lab looking for a terminal. Something in the corner of the room caught her eye.

A scratched 117 with on a Mjolnir chest plate.

He's here, and she would bet that he is raising hell on floor three's med bay. She had to get there.

Just as she was going back to the door control, a sentinel appeared and blocked her path. It spoke no words, but she could only assume that the monitor programmed it to keep an eye on her. Why would she want to keep her and Chief separated?

She eyed the sentinel with malice. Even if she knew how to fight, she did not think it would be in her best interest to start attacking anything in this facility. She was on their good side, for now. Slowly, she picked up a tool that she broke during her fall and walked to an automated repair station on the far corner of the room. The sentinel watched, but made no motion away from the door.

As she began powering up the machine, she slipped into the repair systems programming and began to do some hacking. The sentinel did not look like a typical combat one, so she assumed it belonged to the lab as a tool for manufacturing. After about 20 seconds and a lot of jumping around the system, she was able to confirm her suspicions about the sentinel and take control of it. She reprogrammed it to escort her to the med bay, and she anxiously followed it down the corridor.

She crept through the dark halls, but this time she was not fearful; but excited. She could not wait to see her spartan again. In their final moments after the Composer exploded, she could truly feel the sadness that she had been so desperately trying to keep in since the Dawn. She had already mourned her own life long ago, but she realized in that moment that her death was killing a piece of him.

The hybrid AI could still feel how his armor felt on her fingertips, and she still longed to touch his real skin. She supposed that is the first thing she would do when she saw him. That is, if he trusted her enough to even let her near him. He knew that he was raised with a soldier's mind, and he would probably believe her to be a forerunner trick. She was eager to convince him otherwise.

She chastised herself. He might not be here, and that disturbance on floor three could just be an equipment malfunction. For the first time since High Charity, she reconsidered the idea that she may be facing this fight alone.

Footsteps quickly approaching behind her, followed by hands around her neck forced her out of her thoughts. She was shoved against the wall, and the dumb sentinel who was guiding her flew off into the darkness.

"Identify yourself," The Chief said flatly.

"John! You're really here," Cortana exclaimed in relief.

The Master Chief just stared at her with a blank expression. Her assumption about his lack of trust was correct, so she decided to play along.

"UNSC AI CTN 0452-9," she choked out.

He just eyed her suspiciously. She was sputtering now, so he decided to release his grip but gain closer proximity to determine if she was a threat. Cortana on the other hand was slumped against the wall, breathing heavily, and calling him a bastard under her breath.

"You died," he stated more accusingly.

"Yeah, and you almost just killed me a second time. Anymore questions?" she got out.

"How are you alive?" he said with a guarded tone.

"Well I'm hoping to find out the specifics soon, but basically I was salvaged by the monitor of this facility and placed inside this body. Its my new "storage chip" so to speak," she explained more evenly.

His expression remained neutral. He was not hostile toward her, but he showed no sign of trusting her either. She then decided to follow up with her previous thought, and she touched his chest in the same spot she had previously.

"Wait," she mimicked the words he had said to her in an attempt to thwart the inevitable.

A flash of hurt went across his face, but it was quickly replaced by his neutral expression.

"Are you injured? Why were you in the med bay?" She asked while quickly doing a once over of his large form. She hadn't appreciate how imposing he could be while she was an AI in his good graces.

"No," he curtly replied. "Are you?" he quickly followed up. She took notice of how he glanced at her neck.

"I'm fine, but we need to find out where we are. How long has it been since the Composer was destroyed?" she replied.

"I'm not sure. I woke up here after you left," he stated.

She appreciated his choice to describe her death as if she just left. It was much easier for her to process it that way, and she would bet it was for him too.

An alarm sounded in the building. Before they could react, they were surround by sentinels. The Chief put himself in between Cortana and the sentinels, but before he could defend them; Cortana collapsed.

He turned around to catch her and noticed the syringe-like bullet sticking out of her neck. One came flying at him, but he dodged it with the speed of a spartan.

"Reclaimer! We mean no harm. We have to prepare you and the Intellect for the upcoming mission. Please follow us," the monitor pleaded.

"What mission?" Chief questioned.

"The Gravemind has returned, and we believe that he is targeting the Intellect."


	2. Chapter 2

**I consider myself to be pretty average when it comes to lore knowledge, so forgive me if its not totally right. I also just outright made some things up for the sake of the story, because why not. And to clear some things up, this takes place after the composer was destroyed, but the Master Chief was never recovered by the UNSC. **

Chapter 2

The Chief ended the corridor standoff with the sentinels under the condition that his armor was to be fixed at once, and that Cortana would remain in his sight at all times. He did not fully trust Cortana yet, and he planned on questioning her in private. However, he did not make that known to her or to Ancient Wave; he wanted them to believe that he trusted her. He expertly hid his doubt about Cortana, but his intentions went beyond discovering her integrity.

He'd be lying to himself if he said that he didn't miss her company.

Despite getting her back almost immediately after losing her during the Composer's destruction, he felt that he hadn't had the _real _Cortana in a long time. Their time on Requiem was strained and depressing. And before that, she had been stranded on High Charity at the hands of the Gravemind.

According to Ancient Wave, the Gravemind sent flood dispersal pods to lesser known Covenant planets to ensure the survival of the flood. The Gravemind's physical form was destroyed at the Ark, but since he is a collection of the flood's victims; he can never be truly killed until the flood is extinct. The flood combat forms that were sent to the nearby Covenant planets were implanted with the Gravemind's memories, so that they could restore him. After they conquered the Covenant planets, they commandeered a public transport ship and set their course for a Forerunner research facility. This research facility was a last ditch effort to find a cure for the flood and save their species.

It didn't work.

The facility contained a large amount of flood specimens, some more advanced than the average combat forms they had encountered on halo. Wave informed them that it was imperative to stop them, and the Chief agreed.

Wave also believed that capturing Cortana would be a priority for the new flood army, but they were not aware that she had a human body now. Their first course of action would be uploading a protocol into her system that would be resistant to flood, in theory. The Forerunners had attempted this protocol in their armor systems, and it failed. Wave is confident that he has perfected it, but he is unable to test it.

Cortana planned to intercept the code to this protocol and examine it for her own safety, and of course; her curiosity.

Before she could do any code examination, she was vocal about wanting a real set of clothes. The former AI was not modest, and she really would not have an issue with being somewhat exposed by the gown if it wasn't for how cold it was in the facility. The building was only inhabited by a Forerunner AI and its machines, so she supposed they did not notice that it was barely hovering above thirty degrees in the facility. Her request for clothing was received, and after taking measurements for her; the sentinels floated off to manufacture them. Cortana and the Master Chief were escorted to the room that she originally awoke in, and they were fed aged MRE's that had been salvaged from a pelican long ago.

It was the first time that Cortana had eaten real food, and she was struggling to enjoy it due to the violent shivering of her body. She always envied human's ability to feel the air around them, but in this moment- she felt no jealously whatsoever.

John took notice of her violent shaking, and he felt a wave of protectiveness wash over him. He was kept warm by the biosuit that he insisted on keeping on. Casually, he gestured for her to walk over to him. She initially felt confused, but as soon as she realized what he was planning; she felt as if her skin was on fire.

The spartan pulled her to sit in his lap with her back to his chest and his arms wrapped around her. She instantly felt warmer, and much happier with her situation. She almost hoped that the clothing would take long to be made. As he breathed steadily, she had to force herself not to shudder at feeling his hot breath on her neck. She instantly began to feel a foreign, womanly feeling; but his question immediately snapped her back into the harsh reality.

"How do I know that its really you?" he asked with coldness in his voice.

So, that's how it was gonna be.

She stopped for a moment. How could she prove that it was really her? She could not create a plausible defense knowing that her existence disintegrated into the Promethean data hub that was the Domain?

He went from cradling her to trapping her in his grip. John was not actively hurting her, but he put enough pressure around her to enforce his seriousness. The longer she hesitated, the more suspicious the super soldier became.

"For once, you've left me without an answer Chief. I can understand your fear, and I wish I had a way to prove that I am the same little blue lady in the data chip; but I don't. I'm just here," she said with defeat in her voice.

"I had accepted my fate. Despite being devastated by the idea of leaving you, I knew it was my job to take care of you, and it was the most precious task I was ever given. I don't regret what I did, and I would give my life for you again. " she choked out under the threat of tears.

Before John could respond, the Ancient Wave came floating in, requesting that Cortana get dressed before her body temperature dropped any lower. The Chief released her from his warm grip, and she walked over to the table where her clothes had been placed. He decided to step outside to give her privacy, despite the fact that she didn't seem to care if he saw her naked. He made one last statement on his way out of the door:

"You were wrong about one thing…"

Cortana gulped hard, and she feared what he was going to say next.

"We take care of each other," he spoke confidently before striding out.

Cortana felt warm, and she hadn't even put the clothes on yet.

**I'd love a review!**


	3. Chapter 3

**Thank you for the reviews! It gives me a lot of motivation to write :) **

Chapter 3

Shortly after getting dressed, she was whisked away to be fitted for her armor. The armor was very promethean in nature, and she doubted that the UNSC would even recognize that she was a friendly if they were to have an encounter. She quickly uploaded a UNSC IFF tag, but this did not make her a soldier of the UNSC.

She tried not to think about how they would cross that bridge. At this point, she should have already been decommissioned. Walking around in an artificially made body and speaking a dead AI's thoughts will not play well for her. Even if she were to get the Master Chief's endorsement, the odds of avoiding ONI were slim to none.

That meant she had to make this mission count.

The weight of the armor pulled her out of her worrisome thoughts. However, she quickly realized that she was totally unprepared to actually use her intricate combat armor. Her coordination still needed work, and she was not very strong yet.

Thankfully, she still had her AI capabilities; so she was able to incorporate combat simulations into her physical processes. She had the right moves, but she did not have the balance or strength to preform them effectively.

John was watching her in the corner of the room, and he noted how awkward she appeared in the armor. He walked up to her, and took a swing at her head.

She quickly deflected it, but it was very sloppy and would have left her open for another strike.

"What the hell?!" Cortana roared.

"You need to train," John nonchalantly stated.

She huffed defiantly, but she knew that he was right. At this point, a grunt could've given her a run for her money. The enemies she would be facing in the next few weeks would be much deadlier than that.

"When you block someone, you need to balance yourself and prepare for your next move. You were off balance and unprepared," he said cooly.

He swung again, but this time she was prepared. She blocked him, then shifted her weight to the right and made a strike. He blocked it with ease, but she figured it was better than her last attempt.

"Better," he calmly stated.

They trained for a few more hours. She was no combat prodigy, but she was a fast learner. Despite her improvement, she still had a long way to go. John was planning on putting her through daily conditioning and training.

The duo still had a few weeks until they embarked on their mission. The monitor was attempting to repair the Master Chief's armor without proper schematics, and it was trying to perfect Cortana's immunity algorithim.

* * *

Ancient Wave was monitoring Cortana and the Master Chief very closely. He was still perfecting the immunity algorithim, as well as trying to disguise a single subroutine. After witnessing the video feeds of the two of them, he realized how important this subroutine would be.

The immunity algorithim had a little clause that Cortana would not approve of.

The main purpose of the immunity algorithim was to protect Cortana from getting infected by the flood. It did so by locking her artificial spinal cord when being attacked, and her body had programmed countermeasures to kill the infection form that was attempting to infect her. However, she could still be killed from blunt force trauma from a combat form. The algorithim also protected her from the Gravemind in that it would override in neural processes when in his presence.

Essentially, it would create a sensory buffer when he would speak and interact with her. Like other flood forms, he could still inflict physical damage. But, he could not tamper with her sanity.

At least in theory.

The subroutine that Wave was diligently trying to hide was not one created in malice, but one created with preservation in mind. Wave truly believed that Humanity as a whole was in great danger, and it was imperative that Cortana remain alive for them. He believed that Cortana was more of an invaluable asset than the Master Chief. His algorithim reflected that belief.

He sincerely hoped that both warriors would remain alive. Wave truly believed that they were capable of ushering in an era of peace. However, he knew that the former AI would sacrifice herself for the soldier if it was needed. He watched her admit it on a video feed hours prior. For the sake of the reclaimers, he could not allow that to happen.

His algorithim was capable of seizing control of her neural processes, but it would only do so if triggered by the Gravemind; or a detection of crippling life signs. If Cortana were to pick up on this aspect of the algorithim, he would merely explain it as being a sort of "life saving mode" that would prioritize her safety. However, he hoped that she would not ask at all.

This "mode" would prioritize her safety above all else if her life signs became fatal. This, in theory, would prevent her from being able to sacrifice herself for the Master Chief, or anyone else.

Ancient Wave was not capable of feeling human emotion, but if he was; he would have certainly felt anxiety.

* * *

The next morning, Cortana woke up feeling completely different than the day before. She did not feel fresh, invigorated, healed or any of the other feelings she always assumed humans felt after a night's sleep.

She felt sore as hell.

John was already awake. He appeared to already have done some level of PT in their makeshift quarters. A slight glint of sweat could be seen on his brow, and a tinge of pinkness was present in his cheeks from exertion.

He noticed that she was awake, and he handed her an MRE.

"I'm not hungry," she said flatly.

"You need to eat," he said with no room for argument.

Despite feeling a wave of annoyance, she knew he was right.

"Alright, but don't be mad when I start getting fat," she jabbed while beginning to rise from bed.

Before he could respond to her comment, he was cut off by a sharp feminine yelp. She tried to hold it in, but she was too sore for silence.

John had a slight snicker across his face, but he decided to take a page out of Kelly-087's book.

"Limp over here," He said dryly.

"Why do I feel like you find my pain _amusing_," the last word was spoken with sass.

She dropped her attitude as soon as he gently grabbed her right arm. He stretched it back, gave a few firm squeezes to the stiffest muscles; and then repeated the process on her left arm. She gave out a relieving sigh as a form of gratitude.

"Lay down," he instructed.

She did so. He began stretching her legs and her back, and at this point in her newly acquired life; it was the greatest relief she had ever experienced. The warm presses from his strong hands forced her to hold back a shudder, and she was surprised at how much she physically and mentally surrendered herself to him.

She trusted him more than anyone in the entire galaxy.

Did he trust her?

She was too afraid to ask.

"That was amazing," she muttered.

"Kelly used to do the same to Sam when he would get sore. He tended to over-exert himself," John said with a solemn tone.

Cortana was overwhelmed with sadness in that moment. He had left his spartan brothers and sisters when he was assigned with Cortana. For a time, she pondered if he blamed her for not seeing his spartan family. As the years went on, she realized that he was not a bitter man. In reality, he was barely a man at all.

In many ways, he was more like a machine than his own AI.

He had personality. One of her favorite things about him was his obscure use of humor. It tended to show itself at the strangest times. He did not lack human emotion either. He not only lacked the ability to show his emotion, but he lacked the desire to have emotion at all. He seemed content with being robotic and cold, and that truly puzzled the former machine.

From the time she was created, she craved _real _human emotion. She could not fathom being able of possessing human emotion, and not wanting to use it. Although, she could not fault him for it. His intense indoctrination inhibited his human side.

Cortana hoped to see him happy one day. Truly happy.

But first, she wanted to ensure the eradication of the flood- especially the Gravemind.

And just like that, she experienced her first true desire for revenge.

**I updated this chapter and fixed the breaks. In my uploaded document, I had used *** to signal a scene change. I didn't realize that they didn't upload correctly, creating a cohesion problem. Enjoy!**


	4. Chapter 4

**Anyone have any other good halo fics they would recommend? I'm really getting into fanfiction.**

Chapter 4

Three weeks had gone by since John prodded Cortana into daily training and conditioning. It was a grueling process for the both of them. Cortana was not a whiner, but she had never gone through such an intense objective. She felt herself becoming stronger, but she also felt constant exhaustion. She also believed that she was making progress with John. He seemed more comfortable around her, but she didn't miss the occasional sideways glances he would throw her way. The legendary spartan was notoriously hard-headed. Not even she could change that about him.

"What's on the training docket today?" Cortana asked lightly while sitting up out of her makeshift bed.

Weary eyes met hers, and she knew exactly what happened before he even said anything.

When she was an A.I., she always dedicated a subroutine to monitoring his vital signs. It wasn't irregular for him to abruptly awaken in the middle of the night with an elevated heart rate and spiking body temperature. His brain activity would be all over the place, and she would read him the daily weather patterns of whatever planet they were on or near to calm him down. It was an obscure thing to do, but she knew he wouldn't appreciate any coddling or questions.

She never asked what the nightmares were about, but occasionally he would mutter a few words before jolting himself awake. Usually, they were the names of his spartan siblings. Sam was the most common one muttered. She could only assume the worst.

"Today's weather is probably going to be the same as yesterday; but what the hell do I know?" she said with a hint of playfulness.

He didn't say anything, but he gave her a nod. He never talked about the things that tormented him.

His dreams usually consisted of violent replays of his greatest failures. He replays Guilty Spark charring Johnson to death, the burning surface of Reach, and the most common one: Sam's death. The legendary spartan only saw himself as a man with many losses, and he would never forget the look in Sam's eyes when he was left behind.

This nightmare was different, and it was possibly the most painful one he had ever had.

It was about Cortana. His tortured mind forced him to relive her death, but it projected some of his own thoughts into it. Instead of an emotional goodbye, his longtime companion bitterly sobbed and screamed. She accused him of failing his objective and protecting her. She even doubted herself, citing that she chose the wrong spartan as her caretaker.

After being thrown into a tailspin of sleeping emotions, he finally awoke to her sleeping on the floor near him. It was comforting to see her alive, but also unnerving because of the obvious change.

Cortana always calmed him down with her chatter. He knew that she was aware of his nightmares. John was truly grateful to have her back, but something stopped him from fully allowing himself to go back to the way things were. He subconsciously wondered if it was because he was afraid that if he allowed himself to slip back into their routine; he would be unable to recover if he lost her for good. She had proved to him that she was her old self, but he felt that he was not the soldier that he used to be.

He silently wrestled his thoughts while he ate another old MRE for breakfast. Cortana never asked him what it was that he dreamt about, but a weird part of him wanted her to. He was not insecure, and he never needed validation. But after that dream, he found himself wondering if Cortana really did blame him.

"I can hear you thinking from over here," Cortana said gently.

"Cortana…" He started, but then hesitated as he felt guilt and embarrassment seep in.

"I'm sorry that I failed you. I let the Gravemind hurt you, then I let you die," his voice dying out at the end.

"John…"

"Intellect, the immunity algorithim is finished. It is time for implantation," Ancient Wave interrupted.

"You know the deal. I want to inspect the code," Cortana retorted with annoyance.

"But Intellect, we have very little time-" the monitor frantically started.

"You are wanting to modify my code. That is not something that I take lightly. Take me to a viewing terminal," Cortana said with little room for argument.

The Master Chief began following the intelligent duo out of the room, but Ancient Wave stopped him.

"Reclaimer, your armor has been successfully repaired. We have also implemented some upgrades that we believe will be useful against the flood. Please go to the armory for installment," the monitor informed.

He looked at Cortana, who was still by his side. She gave him a warm look and squeezed his hand.

"I'll let you know when its been reviewed and the implantation process is started," Cortana said in an all business fashion.

He nodded, and began the trip down to the armory.

* * *

It only took forty minutes to find the clause that the monitor had attempted to hide from her. Her discovery angered her to no end, but she knew that the immunity protocol would be paramount to the success of the mission. She decided to load a separate protocol inter her matrix that would counteract the preservation subroutine. It wouldn't eliminate the subroutine as a whole because it could be somewhat useful. It would instead create a filter of what the subroutine could perform. The subroutine would not be able to completely override her system like the monitor had intended.

"Damn lightbulb," Cortana muttered to herself.

"Chief, the code has been reviewed. I had to make some… revisions," Cortana stated hesitantly over the comms.

"On my way," John said a little eagerly. The armor upgrade must have been impressive.

She knew that her revision would disturb his mood. However, she still needed to deal with Wave. He would have access to her entire code during implantation. It would not be difficult for him to delete her defensive subroutine while she was out. Unless…

Quickly, she made a copy of the code and stored it into her files. She hoped that it would be possible for her to implement it herself without any damage.

"Wave, I'm going to survey the weapons while you finish the last of the preparations. Contact me when its time," Cortana lied.

"Very well, Intellect. It should be finished within the hour," the monitor said with a hint of annoyance.

* * *

His armor looked almost brand new. He didn't much care for the monitor or the sentinels, but he couldn't help but appreciate their work. They had upgraded the systems shielding so that the flood infection forms could not lower it by touching him and "popping". The back of his helmet had also been upgraded so that it would lock up if a form tried to puncture him and attack his nervous system. He was essentially immune to becoming infected, but he was still vulnerable to being shot or beaten to death.

More minor upgrades had also been made to his mobility and sensors. He was honestly a little excited to engage into some combat and see what it could do for him.

After getting Cortana's message, he felt a little bit worried. What revision? And will this put her in danger? These thoughts protruded his mind until he received her second message.

"Chief, change of plans. Meet me at the pelican."

"Understood."

He was there within minutes. As soon as he caught sight of her, he could tell that she was distressed.

"I've deactivated the security cameras and have begun looping old footage on the monitor's end. The pelican will also provide some level of secrecy. It should bide us a little time," Cortana said somewhat frantically.

"Time for what?" the Chief questioned.

"We can't trust the monitor. He created a subroutine in the immunity protocol that would completely override my system if I was in danger. It would cause me to forsake the mission and prioritize my own safety over everything; including you. I won't allow it."

"So now what?" he questioned.

"I made a copy of the code and stored it within my system. The protocol as a whole is safe and effective, but I had to eliminate the preservation subroutine. The monitor would know that I created a defensive subroutine it as soon as implantation began. We have to escape before he finishes the start-up procedures and realizes what I've done," Cortana explained.

"You still need your armor. You can't face the flood defenseless," John said with resolution.

"If I can get to a terminal, I can program some sentinels to get it ready. You gather the weapons and ready the pelican. I may be coming in hot," Cortana reasoned as she grabbed a sidearm.

"If you get in trouble-" John started grimly.

"You'll be the first to know," Cortana finished.

John nodded and began gathering all the weapons he could find. Cortana busied herself on the terminal and summoned the nearest sentinels. They quickly whisked her away to be fitted in the armor.

He managed to get all the weapons in order and the engines started up before he heard gunshots.

"Cortana?" He spoke over their comm.

Nothing.


	5. Chapter 5

**Hello halo fans! The semester is back in session and I am doing my absolute best to keep up with this fic. I hope you all enjoy, and please leave a review for my sad little college heart.**

Chapter 5

The quiet of his comms penetrated his biologically enhanced ears. Despite his usual enjoyment of silence, he found himself utterly despising the nothingness that he heard and felt.

_What the hell happened? _The super soldier asked himself. The usually calm spartan began descending into a spiral of thought, and he struggled to get back into his proper mindset.

He did not usually weigh his feelings towards people. His spartan family was all he ever had, and their relationship was always clear. They were siblings, but they were also soldiers. Losing fellow spartans was devastating, but it was a reality that they all made peace with long ago. If one of his siblings were in danger, one the various spartan fireteams would always be there to assist their endangered comrade. He had his fair share of losses- his dreams were a constant reminder of that.

But something about Cortana being endangered felt different. There was no Mjolnir clad family prioritizing her safety. She had no family or friends awaiting her return, and she was not irreplaceable.

_That's not true. _He said to himself. _She's irreplaceable to me._

Yet, that was precisely the problem. She was so unique and held such a high place of importance to the Master Chief -no, to John- that his combat mindset was nearly compromised. His inability to detach himself from her not only put himself in danger, but her as well.

No matter how hard he tried, he could not lay aside his feelings. Although he was a man of flesh and blood, and she was a machine of coding and cloning; he felt as though they were one in the same. They were both Halsey's pet projects that were only built for the war.

But most important of all, they were all each other had.

He reminded himself of that as he sprinted toward the armory guns blazing.

* * *

Cortana took down a small group of sentinels with some well-placed shots. She tried to contain her smug smile, but her pride always got the best of her. It was a fatal flaw. Her excess pride misled her into believing that she could beat the Gravemind on High Charity, and she shuttered at the thought of having to face him again.

_Not now. _She scolded herself. If she didn't focus, she would get herself killed. She couldn't even begin to imagine the shitstorm that would ensue if she died.

_Would John be hurt? _

She chastised herself for selfishly wondering if he would grieve her. Cortana never wanted him to be hurt, but the vain part of herself secretly hoped he would miss her.

_Would he dream about me?_

"Shit!" she yelped.

A stray sentinel on the ground had a little life left it seemed. It spurt off a short beam from the ground and seared her left forearm. The burning pain was unlike anything she had ever felt. Hot tears brimmed the corners of her eyes, but she forced them back in. She silently hoped that there was a burn kit on the pelican. The burn was gnarly to say the least.

_Poor Johnson. _She muttered to herself. The beam only grazed her and it was agonizing. The old soldier must have truly suffered.

The pain brought her back into reality. She needed to focus and get to the armory, then get the hell out of there.

The armory lay in the northern end of a cross shaped halfway. She was approaching from the south, and she approximated that she had a quarter mile sprint down the dark hall. It was time to make the training count.

Within the first fifty feet, she could hear the sentinels buzzing from the eastern corridor. Her artificial heart beat aggressively in her chest. She desperately whipped out her sidearm and got ready for the beams. Facing them was her only choice. She knew what she had to do.

"John, I need you," she urgently requested into her comm.

At the halfway mark, she heard an even larger group of sentinels coming from the western corridor. Her breathing hitched, and she forced her legs to go a little faster. Still no response.

She was getting surrounded. The floating assailants came from behind her. Racing north was her only option. She needed John.

"John!" she screamed into her comm.

The armory door was in sight. Her lungs were on fire, but she couldn't stop. She kept running and taking pot shots when she could. She was 25 meters from the door controls when Ancient Wave descended upon her.

"Intellect! This is a breach of protocol!" he chirped.

Cortana did not have the air to respond. She hit the door control and stumbled into the armory. She ran to her armor stand only to find it completely missing. Before she could assess the situation, she felt a sharp prick in her neck. The world began spinning, and the last thing she saw was a woman with her face; holding a bloody needle.

_John… Where are you? _

She lost consciousness.

* * *

"Cortana, do you read?"

No response.

_She was here. _

Downed sentinels littered the corridors. If he hadn't remembered where the armory was, he could have simply followed the trail of blasted machinery. He'd have to remember to commend her later for her skill, but he had to find her first.

He rounded the final corner and began the sprint down the cross shaped hall. The hall looked untouched. Barren combat zones always left him unnerved, but the sheer emptiness creeped him out a little bit.

He reached the door controls and swiftly activated the button. He immediately noticed a few droplets of blood in the corner near the armor stand. There wasn't enough for it to be a serious wound, but he was concerned, nonetheless.

A fully clad Cortana walked around the corner, and John felt a wave of relief.

"Ready?" he asked with satisfaction.

"Always," Cortana replied evenly.

They made their way back to the bay with no resistance. John had not faced any resistance on his way to the armory, yet he heard some chaos before leaving the pelican.

"Cortana, where is Wave?" The Chief questioned.

"No idea Chief. I killed off a couple sentinels, but that was all I encountered on my journey to the armory," she ended slightly robotically.

"Why did you not respond to my comms?" he prodded while running into the pelican.

"I did not receive any comms. My suit transmitter must be broken. I will repair it once we are in transit," She deadpanned.

"Wait, there is something we must do before we leave," She stated.

Cortana ran out of the pelican with a handful of salvaged pulse grenades. The bay had two other Forerunner ships that looked as though they had not been touched for centuries. Regardless of the age, they still appeared operational.

The armor-clad Cortana climbed atop the ships and placed the grenades directly into the ships' respective power cores and maneuvering mechanisms.

"Cortana! What the hell are you doing?" The Chief demanded.

Cortana steadily planted the grenades into the weak points without explanation. Once they had erupted, she trotted back into the pelican.

"Let's go. The destruction of the flood awaits," She said neutrally.

"Why did you do that? We are wasting time," John asserted.

"In the event that the two experimental flood forms in this facility break loose, we need to ensure that they can't escape," she explained.

"Flood forms are here? Why didn't you tell me?"

She did not respond, but she did climb into the copilot's chair; implying that she was ready to leave.

_Maybe the combat stress got to her. _He reasoned as he strapped himself in.

John masterfully piloted the pelican into atmosphere. Their first stop a small moon outside an abandoned Covenant planet. It had a small population of skirmisher pirates that were believed to have a stockpile of plasma weapons. It was only a day's trip from the Forerunner facility, and it should have a ship that was capable of slipspace travel.

He punched in the coordinates that Cortana gave him, then promptly abandoned the pilot chair. John watched as Cortana repaired her suit transmitter, and not a word passed between them.

* * *

For the second time since her recreation, Cortana groggily awoke from a drug induced sleep on a cold table. She sleepily noted that her left arm was bandaged, and her noticed that she could smell dried up blood as she breathed through her nose. She tried to get off the table, but the wrist and leg restraints left her stationary.

She remembered everything, and panic settled in.

_Where is John?_

_And who is the woman with her face? _

**I hope that wasn't confusing. Stayed tuned ( ͡° ͜ʖ ͡°)**


	6. Chapter 6

**Thanks to all of you who follow/favorite/review. Seeing the notifications honestly make my day 3**

Chapter 6

John was not a social man, and he didn't pretend to enjoy conversations. He kept them curt, but polite. He typically said what he needed to say, and that was that.

Cortana was one of the only people that he enjoyed talking to. He still remained mostly quiet, but he enjoyed her chatter and would often chime in.

Despite his lack of sociability, he was _very _observant. He believed that a lot of people mistook him for either an emotionless meathead, or a robotic freak. He honestly didn't care what they thought. Their lack of knowledge often gave him the upper hand.

Seeking and taking advantage was a value that he had from birth. John was never malice, but he simply loved to win. He often subconsciously analyzed situations for some form of dominion, even if it didn't require any. It was an odd trait, but one that served him well.

However, he simply didn't know how to analyze Cortana's recent behavior. He had seen many soldiers change under pressure, but this was different. She seemed calm as ever, but she would just sit there. Cortana was the most productive being he had ever met. He could hardly imagine her ever sitting there and doing absolutely nothing for an extended period of time.

Even during the rare times when they had no immediate objective, she would busy herself through statistics and analyzation. At the very least, she would have some chatter. Ever since escaping the Forerunner facility, she seemed… distant.

The Spartan didn't know what to think. She had earned his trust during their time at the facility. He didn't even want to entertain the idea that she was somehow compromised. Did she sustain some sort of trauma that he wasn't aware of? Is that why she wasn't herself?

Did the rampancy somehow come back?

The last thought made him sick. Their first rampant experience had been enough to disturb him, and he seriously doubted her could handle seeing her in that level of pain a second time.

As the days past, his worry grew. He couldn't do it again.

* * *

"IFF tag?" Captain Lasky demanded.

"Negative," Ensign Michaels responded.

"What about Cortana? Any emergency communication?" Lasky asked with desperation in his voice.

"Nothing. Both are completely offline," the young Ensign stated.

Lasky began rubbing at his temples. He could hardly believe what had taken place in the short time that he took over command of the Infinity. The "aging" Spartan with the crazy AI turned out to be right, and now the deadly pair were missing.

He knew just as well as everyone else that "Spartans never die" was just a morale booster. Despite the inhuman feats, they were still very human and killable. But the Master Chief, he might as well be immortal.

The man just wouldn't die.

But Cortana? She seemed like she was on her way out. For a moment, the Captain internally pondered.

If Cortana died, would that kill a piece of the stoic Spartan?

He didn't want to know.

* * *

She was expecting some form of torture. Starvation, beating, psychological abuse, anything that a normal POW would expect. But, she wasn't exactly a _normal _POW. This was also proving to be no ordinary war.

She was surprised at the treatment. It wasn't ideal, but it was relatively humane. As long as she obeyed, that is.

"_Where is John?" She screamed at the bobbing monitor._

"_Relax, Intellect. His mission is underway, yours is just beginning. There is much to do if you will be prepared to face the Gravemind," His voice faded as he floated down the hallway._

_Cortana didn't hesitate. She wiggled and writhed until she was able to retrieve the data pad out of her pocket. The sentinel that she had previously hacked was by her side in minutes. She had almost made it to the bay before she was caught._

_They rushed her into the medical bay, but Wave injected her with serum that ignited every nerve ending in her body. It lasted for hours._

Her daily routine had been fairly monotonous. She woke up, trained to the best of her ability, and endured whatever obscure tasks had been laid out before her.

One day it was coding a repair systems manual. Another day it was salvaging UNSC parts out of old crates. Some days she just sat there, but regardless of the task- it all felt pointless. It was boring, and nothing pertinent to the mission had come up yet. She could only assume that Ancient Wave was merely trying to keep her busy.

Meanwhile, she was secretly attempting to gain control of the facilities long range security system so she could triangulate John's pelican. She sometimes fearfully entertained the idea that he was coming back, but she deemed it as highly unlikely.

She concluded that he would not risk coming back here. Even if he did figure out that his companion was not her, she figured that he would likely assume that her existence had been false this whole time. Despite his often overlooked intelligence, she seriously doubted that he would figure out that _she _was a clone.

Cortana's eventual realization saddened her. As the days past, she came to terms with the face that John may never trust her again after this- assuming they both lived long enough for a reunion.

A message notification on her data pad derailed her moping. Her original data pad had been confiscated after he attempted escape, but she managed to steal a malfunctioned one. After some tinkering, she was able to repair it so that it was mostly functional.

The message was sent by an anonymous sender, which confused her. It only contained the word "haven" followed by the coordinates for a location off facility. She had no earthly idea who could have known how to reach her.

Was it John?

No, that's impossible. Encryption of this level on a forerunner channel was something she could barely do, let alone a Spartan with no previous experience of programming.

It had to be a forerunner.

Was it a trap laid by the Didact? Or was this Ancient Wave's way of testing her? The possibilities ran buck wild through her head, but they suddenly halted at one hopeful conclusion.

The Librarian.

**Not much action in this chapter. I'm trying to set up the rest of the story without rushing or skipping anything. Hope you enjoyed!**


	7. Chapter 7

**This is another set-up type chapter. The one after will have some action, I promise. **

Chapter 7

**Unknown Forerunner Research Facility, 4 days before escape**

Ancient Wave floated around his creator's study in consistent circles. He dedicated subroutines to monitor his motor functions, and he made sure his circular path was precise down to the nanometer. Precision was everything, and control was addicting. The monitor had been alive for thousands of years; enduring many circumstances that he had little control over. However, only one circumstance continued to influence him.

Wave carried the memory of his creator's death like a slave heaving brick. The slave could throw the brick away, but at what cost? He so desperately wanted to delete it from his core memory, but he simply couldn't. The cost of losing such a memory, and the lessons that came with it; simply outweighed the benefits.

The scarring memory of losing a sentient that he cared about is what compelled him to revive Cortana in the first place. Although it was agonizingly painful, it gave him a sense of morality. It kept him grounded in the floating depths of space. Reality often felt like a balloon ascending into the heavens, leaving him grasping at the string.

He resurrected the most powerful AI of human origin, gave her a body and revitalized her ambition. Having the power to create such a capable being invigorated him, but also scared him. He knew that he was at risk of being overthrown, but he hoped that the flood uprising would take precedents over Cortana's potential need for revenge.

Wave also went out of his way to retrieve her human companion, but quickly realized that was a mistake. He believed that he could control the situation. The Master Chief was but a man, while the monitor was created with perfection in mind.

What he failed to account for was emotion. He was unaware that the AI and the soldier had formed such a bond on the battlefield. The bond itself was unsurprising, but the _nature _of the bond is what caught him by sheer surprise.

He had expected to see a creator/created relationship, or perhaps even a sort of working friendship. But both of those options had platonic undertones. What he had observed through the security system was anything but platonic.

Given the simplicity of the human brain, he could have predicted some level of sexual attraction among the pair. However, the AI and the soldier showed signs of being beyond mating partners- they were similar to the life-bonded.

He was confident that Cortana was the Intellect, but he was uncertain if the Master Chief was truly the Warrior. The monitor could not accept that the Warrior would be a human. It seemed preposterous.

Preposterous, but not entirely impossible. He had to test them; it was the only way. Sending them in against the flood without fully knowing if he was dealing with the actual Warrior and Intellect would only weaken their already dismal chances.

"S-762 to W-045, the secondary form is complete and prepared for activation. Units will remain in standby until further action required."

The message broke his circular tract. Wave immediately began the quick descend to the main lab to finalize his second creation. His test would be dangerous, but it was the only way to test their bond. The Master Chief, in particular.

* * *

**UNSC Salvage Pelican, 68 hours from destination **

Cortana's chatter had gradually returned, but it lacked the same vitality that it had previously. It wasn't unusual for her to question something rather arbitrary, work some sort of angle on the problem, and then ask his opinion on the matter. It was strange, and sometimes distracting; but it grew on him early on.

Now, she pondered some rather shallow things. Instead of trying to absentmindedly create a new calendar system for the outer colonies, she would question what snow feels like. She had questioned what the sun felt like during her late stage of rampancy, but this was different. She hadn't put any sort of complex spin on it, she genuinely sounded like she was at a loss.

He hadn't slept much during the last few days of travel, but she had slept almost systematically. During her rest, she hardly moved. On the installation, she would toss and turn. He had to say something.

"Have you been able to get a scan on the Covenant planet?"

He instantly wanted to slap himself in the face. Demanding another task from her was not getting him anything useful.

"We are still too far out. I likely won't be able to detect anything for another 48 hours," Cortana responded lightly.

Chief pondered for a moment. Her tone sounded pleasant enough, but she seemed a little off kilter. Almost like she wasn't paying attention.

* * *

She wasn't. The clone had been feeling overwhelmed for the last several days. She was born, given only a day of freedom; then she was tormented with all the data.

Her creators had not given her every piece of Cortana, because that simply would not have been feasible. She received copies of Cortana's significant behavior patterns and memories that had been collected from her time in the Domain.

Unfortunately, they had unintentionally downloaded some of Cortana's hinderances. Only a fellow AI could detect such baggage. Aside from minimal things, such as random fixations on irrelevant human function, she only had one major flaw.

Cortana's attraction to the Master Chief made her a more vulnerable AI. The childish love she held for the soldier was a typical inherited human weakness.

"Are you okay?" The Master Chief asked with a gentle tone.

He must've seen the slight bewildered look on her face, because he clarified before she could respond.

"You've seen a little off since we left. I know you really suffered on Requiem, and now you are here on another mission…" He drifted off, clearly feeling awkward and unsure of how to finish.

"I'm a little fatigued, but the mission comes first, right?" she added a small smile at the end.

The answer seemed to satisfy the Master Chief enough. After a moment of silence, he quietly made his way back to the copilot chair. She thought he might say something else, but he must've felt too awkward.

Controlling her inherited feelings was extremely difficult. She always had some foreign desire to go be around him, or talk to him about random things. The clone would do these things to maintain the façade that she was Cortana, but she felt unconvincing. Sometimes, she could almost feel him studying her. He was a very untrusting person by nature.

Yet, something about him was very intriguing. She knew very little about the man in the armor. The majority of his personal files remained unrecovered. Cortana kept those closely guarded, and she had managed to not relinquish them into the data pit that was the Domain.

The clone would keep acting, and when the time was right; she would fulfill her purpose.

* * *

**Unknown Forerunner Research Facility – 2 days after message **

She had the coordinates memorized. When she was feeling especially hopeless, she would recite it; almost like a mantra. Fortunately, she had a plan.

While preforming some maintenance on a minor piece of the facilities pressurizing system, she had to make some trips down to the salvage unit. She was escorted by sentinels everywhere she went, but the security detail doubled on these trips.

Most of it was junk, but there was enough functioning equipment to complete the repair. While sifting through the hoard of machinery, a large piece of equipment caught her eye. She scanned the room, and she noticed that the sentinel babysitters were keeping a watchful eye on her.

Cortana decided to take a calculated risk. If she programmed them to go idle for a few minutes, while activating a nearby group of sentinels to travel on the path they should be taking to get back to her repair station; Wave would likely not notice the discrepancy.

She found her data pad, and after a couple taps; the plan was set into motion. She darted to the corner of the room and cleared off the hunk of metal. It was significantly damaged, and for a second she wasn't sure what it was.

She found an old UNSC escape pod. It resembled one from The Pillar of Autumn, but she doubted it could have actually come from that far away. Abruptly, she ran a system check and found that the engines were offline. She predicted this, as they were only meant to travel short distances.

Cortana wasn't able to do a full diagnostic of the pod's status, but she had a general idea of what it needed. Mentally, she made a checklist of what she would need to not only fix the engines, but she needed to upgrade them enough to get her to the Librarian's location.

She noted that five minutes had passed since deactivating the sentinels. It was time to return back to work, but this time; she had a real purpose. The sentinels led her away, and she could barely contain a victorious grin.

**Some unfortunate news for this story; I will be leaving for basic training in January. I will not be returning until late April/ early May. I am gonna try to knock out some more chapters after I finish with finals, so bear with me! Thanks for reading!**


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